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Run Parallelized BLAST

Source: R/parallel_blast.R
parallel_blast.Rd

Run parallel BLAST for a set of sequences

Usage

parallel_blast(
  query_seqs,
  db_path,
  ...,
  total_cores = 1L,
  num_threads = 1L,
  blast_type = "blastn",
  perc_id = 80L,
  perc_qcov_hsp = 80L,
  num_alignments = 4L,
  retry_times = 3L,
  mt_mode = c("2", "1", "0"),
  verbose = c("progress", "silent", "cmd", "output", "full"),
  env_name = "blastr-blast-env",
  asvs = deprecated(),
  out_file = deprecated(),
  out_RDS = deprecated()
)

Arguments

query_seqs

Character vector with sequences.

db_path

Path to the formatted BLAST database.

...

These dots are for future extensions and must be empty.

total_cores

Number of parallel BLAST processes to run.

num_threads

Number of threads/cores to run each BLAST process on.

blast_type

BLAST+ executable to be used on search.

perc_id

Lowest identity percentage cutoff.

perc_qcov_hsp

Lowest query coverage per HSP percentage cutoff.

num_alignments

Number of alignments to retrieve results for each query sequence. Defaults to 4.

retry_times

Number of times to retry failed BLAST jobs. Defaults to 3 attempts.

mt_mode

Multithreading mode to be used by BLAST+. One of: c("2", "1", "0"). See BLAST+ manual for details.

verbose

Strategy used for showing outputting internal commands. Defaults to "progress".

env_name

The name of the conda environment used to run command-line tools. Defaults to "blastr-blast-env".

asvs

Deprecated. Same as query_seqs. Use query_seqs instead.

out_file

Deprecated. Path to output .csv file on an existing directory.

out_RDS

Deprecated. Path to output RDS file on an existing directory.

Value

A tibble with the BLAST tabular output.

Examples

if (FALSE) { # \dontrun{
dna_fasta_path <- fs::path_package(
  "BLASTr", "extdata", "minimal_db_blast",
  ext = "fasta"
)
temp_db_path <- fs::path_temp("minimal_db_blast")
make_blast_db(fasta_path = dna_fasta_path, db_path = temp_db_path)
asvs_string <- c(
  "CTAGCCATAAACTTAAATGAAGCTATACTAA",
  "ACTCGTTCGCCAGAGTACTACAAGCGAAAG"
)
blast_res <- parallel_blast(
  query_seqs = asvs_string,
  db_path = temp_db_path
)
blast_res
} # }